Package meshi.energy.solvate

Class Summary

SigmaParameters	All the atom type specific parameters of a solvation sigma function
SolvateCreatorHBforMinimization	The different between this creator and the "SolvateCreatorRegularHB" (see the latter main comment for a lot of details), is in the way the hydrogen-bond distance sigmoid is set.
SolvateCreatorLongHB	The different between this creator and the "SolvateCreatorRegularHB" (see the latter main comment for a lot of details), is in the way the hydrogen-bond distance sigmoid is set.
SolvateCreatorRegularHB	The Creator class for setting up an instance of SolvateEnergy as described in Kalisman & Keasar (2008).
SolvateDistanceAttribute	In the SolvateEnergy evaluation function these fields are to be recalculated for EVERY distance in the non-bonded list.
SolvateDistanceAttributeBetweenPolars
SolvateDistanceAttributeCreator
SolvateDistanceAttributeNonPolarPolar
SolvateDistanceAttributePolarNonPolar
SolvateDistanceAttributeWithAhydrogen
SolvateDistanceAttributeWithNonPolar
SolvateEnergy	The implementation of the cooperative solvation term for proteins as described in Kalisman & Keasar (2008).
SolvateParametersList	The parameter class required for the SolvateEnergy class.

Enum Summary

SolvateDistanceType	Distances are treated differently by Solvate Energy.
SolvateEnergy.SuperType	Setting the general type for each atom in the atom list: (0) Carbon (1) Backbone polar, (2) Sidechain polar (3) Hydrogens This is done to save time on type checking.